Monday, 27 August 2012

The laser scanning of fossil type specimens at BGS and our
partner organisations in the JISC funded project is progressing well, with some stunning results. BGS now has
several hundred specimens completed, in addition to those being scanned by our
partner organisations.

Michela Contessi, one of the project team,
operating the NextEngine HR Laser Scanner

Whilst the formal launch of the project website, with the database and portal to all the type specimen data, images, 3D anaglyphs and 3D digital models, is still almost a year away, I thought it would be useful to make a selection of digital models available for users to download, experiment with and comment on.

Please note: All the digital models are licensed under a Creative Commons Attribution-non Commercial-ShareAlike license.

Instructions for
downloading and viewing models

1.The models are available for downloading from
the BGS FTP server. Go to ftp://ftp.bgs.ac.uk/pubload/mhowe/GB3D_TypeFossils/and download as many as you like. All
the models are in “.PLY” format. This format is known as the “Polygon File
Format” or “Stanford Triangle Format” and is a particularly simple and space
efficient way of storing 3D scanned data.

2.Each model is numbered with its specimen
registration number. To obtain the metadata for each specimen (i.e. identification,
locality, age, etc), visit the BGS PalaeoSaurus database at http://www.bgs.ac.uk/palaeosaurus/home.cfm
. Enter the registration number into the appropriate box on the search form
(the bottom box). Registration numbers consist of one or more letters followed
by a number. DO NOT leave a space between the letters and the numbers and
ensure you enter the correct case (upper or lower case - capital or small
letters).

3.I recommend either MeshLab or SpiersView for
viewing the models. Both are easily available as free downloads from the web.

4.MeshLab can be downloaded from: http://meshlab.sourceforge.net/. MeshLab is a particularly useful tool
for viewing and improving models and changing file formats.It can also be used to measure distances
between points of the displayed meshes and to export planar sections of a mesh
in SVG format.

5,SpiersView can be downloaded from http://spiers-software.org/ . SpiersView
is particularly useful for viewing models as coloured anaglyphs, i.e. they
appear in full 3D when viewed through red – cyan glasses. SpiersView needs a
VAXML file for each .PLY file.

Cut and paste the following into a basic
text editor:

<?xml version='1.0'?>

<vaxml>

<header>

<version>2</version>

<title>Minimal VAXML
example</title>

</header>

<objects>

<object>

<name>Single Object</name>

<file>GSE 482.ply</file>

<material>

<colour>

<red>255</red>

<green>255</green>

<blue>255</blue>

</colour>

</material>

</object>

</objects>

</vaxml>

Replace the file name (in this case GSE 482.ply) with the name of the file you wish to
view and save with the file name suffixed with .vaxml (eg. GSE 482.vaxml).When running SpiersView, you should then open
the .vaxml file to open the corresponding .ply file. The advanatages of vaxml
are explained on the SpiersView Site.

Adam Smith, who joined the project team in May, has just
moved on to become Collections Access Officer [Natural Sciences] with
Nottingham City Council, based at Wollaton Hall Museum. This is a permanent
curatorial post, and I congratulate Adam on his success.

Adam setting up the NextEngine HR Laser Scanner on a type
fossil from the BGS Collections

Adam
commented, just before he left the project team:

“I’ve
always been fascinated by fossils and wanted to be a palaeontologist from an
early age. I completed degrees in palaeontology at Portsmouth and Bristol and
then continued my studies in Dublin, where I conducted a PhD project specialising
on plesiosaurs. Plesiosaurs are extinct marine reptiles that inhabited the
ocean during the age of the dinosaurs.

I
am pleased to have been part of the JISC digitisation project, working with fossils
every day. The 3D models and photographs we are producing will be a valuable scientific
and educational resource for everyone from academic researchers to school
children. I’m sure I’ll use them myself!”

The other member to join the team at the same
time as Adam was Michela Contessi, who is just completing a PhD at the
University of Bologna on vertebrate ichnofossil assemblages in the Tataouine
basin (South Tunisia). She has considerable experience on a number of laser
scanners, including the NextEngine and has put her expertise to good use in the
project.

The project lab, showing the two Canon EOS5D
cameras in the fore- and mid- ground and
one of the NextEngine HR Laser Scanners at the back, being operated by Michela. Note the “see-saw” on the camera copy
stand for taking stereo photographs, and the greyscale. The cameras are
controlled by computers and the digital images are transferred directly to the
BGS SAN (Storage Area Network = corporate disc storage).

Sunday, 26 August 2012

Two local geological societies, the Leicester Literary and
Philosophical Society and the Warwickshire Geological Conservation Group,
visited the Geological Collections at BGS on a sunny Saturday in August. In the
morning, Dr Phil Wilby showed them the work that BGS has been doing on the
Ediacaran (Neoproterozoic, Precambrian) fossils of Charnwood Forest. This work
centres around new sets of moulds and casts that BGS has produced, in
conjunction with GeoEd and Natural England. At one locality, approximately 140m2
of casts have been made, making it probably the largest exercise of its
type anywhere in the world. Studying the casts under controlled lighting in the
laboratory provides much more information than can be seen at outcrop.

Viewing
one of the three core storage halls at BGS. This one contains material from 15,000
onshore boreholes. [Photo: Mike Clarke]

I then showed the societies round other parts of the
Collections, including the GB/3D scanning and imaging lab. Here they donned 3D
glasses and enjoyed some of the delights of the BGS type fossil collections, while I explained how laser scanning works. There was a lot of interest in
the digital models and I offered to make a selection of models available for
download before the official launch of the main project website next year.

The Warwickshire and Leicester groups put their 3D glasses on to view some of the digital models.

After lunch out in the sun, the group then viewed the
recently open Geological Walk http://www.bgs.ac.uk/contacts/sites/keyworth/geologicalWalk/home.htmland endeavoured to identify the many
different rocks – before receiving copies of the guide. Then, after the group
photograph in front of the James Hutton building, which forms part of the walk, everyone
dispersed.

﻿﻿﻿﻿﻿﻿﻿﻿﻿

Members
of the two societies pose for the group photograph in front of the James Hutton
building. The wall behind the group represents Hutton’s unconformity at Siccar
Point, Berwickshire, Scotland, where gently sloping beds of Devonian to lower
Carboniferous sandstone overlie near
vertical beds of Silurian grewacke. [Photo: Mike Clarke]